Compounds for the treatment of hepatitis C

ABSTRACT

The disclosure provides compounds of formula I, including pharmaceutically acceptable salts, as well as compositions and methods of using the compounds. The compounds have activity against hepatitis C virus (HCV) and may be useful in treating those infected with HCV.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. provisional application Ser. No. 61/540,290 filed Sep. 28, 2011.

BACKGROUND OF THE INVENTION

The disclosure generally relates to the novel compounds of formula I including pharmaceutically acceptable salts, which have activity against hepatitis C virus (HCV) and are useful in treating those infected with HCV. The disclosure also relates to compositions and methods of using these compounds.

Hepatitis C virus (HCV) chronically infects an estimated 170 million people worldwide, with 3 to 4 million infected individuals in the United States alone (Boyer, N. and Marcellin, P. J. Hepatology. 2000, 32:98-112; Alter, M. J., et al. Engl. J. Med. 1999, 341:556-562). Prior to the mid 1990s, transfusion with infected blood products was the main route of HCV transmission. Following the introduction of blood screening methods, transmission via injection drug use became the primary risk factor. Chronic infection often leads to the development of severe liver complications, including fibrosis, cirrhosis, and hepatocellular carcinoma. HCV infection is also the leading cause of orthotopic liver transplantation in the United States. The degree to which disease progression is related to viral and cellular factors is not completely understood.

Considerable heterogeneity is found within the nucleotide and encoded amino acid sequence of the HCV genome (Simmonds, P. J. Gen. Virology. 2004, 85:3173-3188). Based on this sequence diversity, six major genotypes and multiple associated subtypes have been described. The genotypes of HCV differ in their worldwide distribution, and the clinical significance of the genetic heterogeneity of HCV remains elusive despite numerous studies of the possible effect of genotypes on pathogenesis and therapy.

Medical treatment for HCV is limited by the lack of a vaccine or approved therapies that specifically target the virus. Currently, patients undergo treatment with a combination of parenterally administered pegylated alpha-interferon and oral ribavirin. Genotype 1 HCV is the most difficult to treat and elimination of the virus (sustained virologic response) is achieved for only approximately 50% of patients (Fried, M. W. et al. N. Engl. J. Med. 2002, 347:975-982; Zeumzem, S, Nature Clinical Practice. 2008, 5:610-622). This poor treatment response, combined with often severe side effects induced by therapy, highlight a need for improved antiviral drugs with better efficacy and safety profiles.

HCV is a member of the Flaviviridae family of viruses with a single-stranded positive-sense RNA genome. Following infection of host cells, the 9.6 Kb genome is translated into a polyprotein precursor of approximately 3,000 amino acids (reviewed in Lindenbach, B. D. and Rice, C. M. Nature. 2005, 436:933-938; Moradpour, D, Penin, F., and Rice, C. M. Nature Reviews. 2007, 5:453-463). Post-translational processing by both cellular and viral proteases results in the generation of at least 10 separate viral proteins. The structural proteins (which by definition are found in mature virions) include core, E1, E2, and possibly p7, and originate from the amino-terminal region of the polyprotein. The core protein assembles into the viral nucleocapsid. The E1 and E2 glycoproteins form heterodimers that are found within the lipid envelope surrounding the viral particles, and mediate host cell receptor binding and entry of the virus into cells. It is unclear if p7 is a structural protein, and its role in replication has yet to be defined. However p7 is believed to form an ion channel in cellular membranes, preventing acidification of intracellular compartments in which virions are assembled, and it has been shown to be essential for viral replication and assembly. The nonstructural proteins NS2, NS3, NS4A, NS4B, NS5A, and NS5B are produced through maturational cleavages of the carboxy-terminal region of the polyprotein. NS2 along with the amino terminus of NS3 form the NS2-3 metalloprotease which cleaves at the NS2-NS3 junction. Additionally, NS2 is involved in assembly and egress of nascent virions. The NS3 protein contains both a serine protease in its amino-terminal region, and a nucleotide-dependent RNA helicase in its carboxy-terminal region. NS3 forms a heterodimer with the NS4A protein, constituting the active protease which mediates cleavages of the polyprotein downstream of NS3, both in cis, at the NS3-NS4A cleavage site, and in trans, for the remaining NS4A-NS4B, NS4B-NS5A, NS5A-NS5B sites. The complex formation of the NS3 protein with NS4A seems necessary to the processing events, enhancing the proteolytic efficiency at all of the sites. The NS3 protein also exhibits nucleoside triphosphatase and RNA helicase activities. The NS4B protein has been shown to be important for localization of HCV proteins into replication complexes in altered membranous structures within the cell. NS5B encodes an RNA-dependent RNA polymerase that is involved in the replication of HCV.

Subgenomic HCV replicons, containing the untranslated regions 5′ and 3′ to the coding sequence fused to the nonstructural proteins or the full-length polyprotein, are competent for translation, viral protein expression, and replication within cultured cells (Lohmann, V. et al. Science. 1999, 285:110-113; Moradpour, D, Penin, F., and Rice, C. M. Nature Reviews. 2007, 5:453-463). The replicon system has proven valuable for the identification of inhibitors targeting the nonstructural proteins associated with these functions. However, only limited subsets of HCV genotypes have been used to generate functional replicons.

Other systems have been used to study the biology of the HCV structural proteins that mediate the entry into host cells. For example, virus-like-particles made in recombinant baculovirus-infected cells with the HCV core, E1 and E2 proteins have also been used to study the function of the HCV E1 and E2 proteins (Barth, H., et al. J. Biol. Chem. 2003, 278:41003-41012). In addition, pseudotyping systems where the E1 and E2 glycoproteins are used to functionally replace the glycoproteins of retroviruses have been developed (Bartosch, B., Dubuisson, J. and Cosset, F.-L. J. Exp. Med. 2003, 197:633-642; Hsu, M. et al. Proc. Natl. Acad. Sci. USA. 2003, 100:7271-7276). These systems yield HCV pseudoparticles that bind to and enter host cells in a manner which is believed to be analogous to the natural virus, thus making them a convenient tool to study the viral entry steps as well as to identify inhibitors block this process.

Recently, a full-length genotype 2a HCV clone, JFH1, was isolated and demonstrated the ability to replicate in vitro. Through repeated passage and adaptation in cell culture increased titers of infectious virus were produced (Lindenbach, B. D., et al. Science. 2005, 309:623-626; Wakita, T. et al. Nature Med. 2005, 11:791-796). In contrast to the HCV replicon or pseudotyping systems, the infectious virus is useful for studying the complete HCV replication cycle, including identifying inhibitors of not only the replication proteins, but those involved in early steps in virus infection (entry and uncoating) and production of progeny viruses (genome packaging, nucleocapsid assembly, virion envelopment and egress).

Triazines have been disclosed. See WO 2009/091388 and US 2009/0286778.

The invention provides technical advantages, for example, the compounds are novel and are effective against hepatitis C. Additionally, the compounds provide advantages for pharmaceutical uses, for example, with regard to one or more of their mechanism of action, binding, inhibition efficacy, target selectivity, solubility, safety profiles, or bioavailability.

DESCRIPTION OF THE INVENTION

One aspect of the invention is a compound of formula I

where Ar¹ is phenylene or pyridindiyl substituted with 1 R²; R¹ is alkyl, hydroxyalkyl, alkoxyalkyl, haloalkyl, cycloalkyl, hydroxycycloalkyl, alkoxycycloalkyl, halocycloalkyl, cycloalkenyl, benzyl, indanyl, or alkylcarbonyl; R² is hydrogen, cyano, halo, alkyl, haloalkyl, alkoxy, or haloalkoxy; R³ is hydrogen, alkyl, (amino)alkyl, (alkylamino)alkyl, (dialkylamino)alkyl, ((alkylcarbonyl)amino)alkyl, ((haloalkylcarbonyl)amino)alkyl, ((alkoxycarbonyl)amino)alkyl, ((benzyloxycarbonyl)amino)alkyl, alkylcarbonyl, alkoxycarbonyl, benzyloxycarbonyl, aminocarbonyl, alkylaminocarbonyl, or dialkyaminocarbonyl; R⁴ is hydrogen, alkyl, (amino)alkyl, (alkylamino)alkyl, or (dialkylamino)alkyl; R⁵ is hydrogen, alkyl, (amino)alkyl, (alkylamino)alkyl, or (dialkylamino)alkyl; Q is an alkylene or alkenylene chain containing 0-6 groups selected from the group consisting of O, NR³, S, S(O), S(O₂), C(O)O, C(O)NR⁴, OC(O)NR⁴, NR⁴C(O)NR⁴, and Z, provided that any O or S atom does not directly bond to another O or S atom, such that ring A is 13-36 membered; and where the alkylene or alkenylene chain is substituted with 0-6 substituents selected from the group consisting of alkyl, alkylene, hydroxy, and alkoxy; X is O, CH₂, CO, CO₂, or C(O)NR⁵; and Z is C₃₋₇cycloalkylene or phenylene; or a pharmaceutically acceptable salt thereof Another aspect of the invention is a compound of formula I where Ar¹ is phenylene or pyridindiyl substituted with 1 R²; R¹ is haloalkyl; R² is hydrogen or halo; R³ is hydrogen or alkyl; R⁵ is hydrogen or alkyl; Q is an alkylene or alkenylene chain containing 0-6 groups selected from the group consisting of O, NR³, and Z, provided that any O atom does not directly bond to another O atom, such that ring A is 13-36 membered; and where the alkylene or alkenylene chain is substituted with 0-6 substituents selected from the group consisting of alkyl and alkylene; X is C(O)NR⁵; and Z is C₃₋₇ cycloalkylene or phenylene; or a pharmaceutically acceptable salt thereof. Another aspect of the invention is a compound of formula I where Ar¹ is 1,4-phenylene or 1,4-dipyridindiyl substituted with 1 R²; R¹ is trifluoroethyl; R² is hydrogen or fluoro; R³ is hydrogen; R⁵ is hydrogen; Q is an alkylene or alkenylene chain containing 0-6 groups selected from the group consisting of O, NR³, and Z, provided that any O atom does not directly bond to another O atom, such that ring A is 13-36 membered; and where the alkylene or alkenylene chain is substituted with 0-6 substituents selected from the group consisting of methyl and methylene; X is C(O)NR⁵; and Z is C₃₋₇ cycloalkylene or phenylene; or a pharmaceutically acceptable salt thereof.

Another aspect of the invention is a compound of formula I where ring A is 13-36 membered.

Another aspect of the invention is a compound of formula I where ring A is 20-30 membered.

Another aspect of the invention is a compound of formula I where ring A is 23-24 membered.

Another aspect of the invention is a compound of formula I where Ar¹ is 1,4-benzenediyl substituted with 1 R²; or a pharmaceutically acceptable salt thereof.

Another aspect of the invention is a compound of formula I where Ar¹ is 1,4-dipyridindiyl substituted with 1 R²; or a pharmaceutically acceptable salt thereof.

Another aspect of the invention is a compound of formula I where Z is 1,4-phenylene; or a pharmaceutically acceptable salt thereof.

Another aspect of the invention is a compound of formula I where Z is cyclopropylene; or a pharmaceutically acceptable salt thereof.

Any scope of any variable, including R¹, R², R³, R⁴, R⁵, Ar¹, Q, X, and Z, can be used independently with the scope of any other instance of a variable.

Unless specified otherwise, these terms have the following meanings. “Halo” means fluoro, chloro, bromo, or iodo. “Alkyl” means a straight or branched alkyl group composed of 1 to 6 carbons. “Alkenyl” means a straight or branched alkyl group composed of 2 to 6 carbons with at least one double bond. “Cycloalkyl” means a monocyclic ring system composed of 3 to 7 carbons. “Alkylene” means a straight or branched divalent alkyl group composed of 2 to 36 carbons. “Alkenylene” means a straight or branched divalent alkyl group composed of 2 to 36 carbons with at least one double bond. For ring A, Y is an alkylene or alkenylene chain with sufficient carbons and optionally other defined groups to form a 13-36 membered ring. “Cycloalkylene” means a divalent cycloalkane moiety composed of 3 to 7 carbons and includes gem-divalency (for example 1,1-cyclopropanediyl) as well as non-gem-divalency (for example, 1,4-cyclohexanediyl). “Alkylidinyl” means a divalent alkene substituent where the divalency occurs on the same carbon of the alkene. “Hydroxyalkyl,” “alkoxy” and other terms with a substituted alkyl moiety include straight and branched isomers composed of 1 to 6 carbon atoms for the alkyl moiety. “Haloalkyl” and “haloalkoxy” include all halogenated isomers from monohalo substituted alkyl to perhalo substituted alkyl. “Aryl” includes carbocyclic and heterocyclic aromatic substituents. Phenylene is a divalent benzene ring. Ar¹ is a divalent heteroaryl ring with respect to forming ring A as in formula I with the substituent R². “1,4-Phenylene” means 1,4-benzenediyl with respect to regiochemistry for the divalent moiety. Parenthetic and multiparenthetic terms are intended to clarify bonding relationships to those skilled in the art. For example, a term such as ((R)alkyl) means an alkyl substituent further substituted with the substituent R.

The substituents described above may be attached at any suitable point of attachment unless otherwise specified. However, it is understood that the compounds encompassed by the present invention are those that are chemically stable as understood by those skilled in the art. Additionally, the compounds encompassed by the present disclosure are those that are suitably stable for use as a pharmaceutical agent.

The invention includes all pharmaceutically acceptable salt forms of the compounds. Pharmaceutically acceptable salts are those in which the counter ions do not contribute significantly to the physiological activity or toxicity of the compounds and as such function as pharmacological equivalents. These salts can be made according to common organic techniques employing commercially available reagents. Some anionic salt forms include acetate, acistrate, besylate, bromide, camsylate, chloride, citrate, fumarate, glucouronate, hydrobromide, hydrochloride, hydroiodide, iodide, lactate, maleate, mesylate, nitrate, pamoate, phosphate, succinate, sulfate, tartrate, tosylate, and xinofoate. Some cationic salt forms include ammonium, aluminum, benzathine, bismuth, calcium, choline, diethylamine, diethanolamine, lithium, magnesium, meglumine, 4-phenylcyclohexylamine, piperazine, potassium, sodium, tromethamine, and zinc.

Some of the compounds of the invention possess asymmetric carbon atoms (see, for example, the structures below). The invention includes all stereoisomeric forms, including enantiomers and diastereomers as well as mixtures of stereoisomers such as racemates. Some stereoisomers can be made using methods known in the art. Stereoisomeric mixtures of the compounds and related intermediates can be separated into individual isomers according to methods commonly known in the art. The use of wedges or hashes in the depictions of molecular structures in the following schemes and tables is intended only to indicate relative stereochemistry, and should not be interpreted as implying absolute stereochemical assignments.

The invention is intended to include all isotopes of atoms occurring in the present compounds. Isotopes include those atoms having the same atomic number but different mass numbers. By way of general example and without limitation, isotopes of hydrogen include deuterium and tritium. Isotopes of carbon include ¹³C and ¹⁴C. Isotopically-labeled compounds of the invention can generally be prepared by conventional techniques known to those skilled in the art or by processes analogous to those described herein, using an appropriate isotopically-labeled reagent in place of the non-labeled reagent otherwise employed. Such compounds may have a variety of potential uses, for example as standards and reagents in determining biological activity. In the case of stable isotopes, such compounds may have the potential to favorably modify biological, pharmacological, or pharmacokinetic properties.

Biological Methods

Infection assays. HCV pseudoparticles, produced using standardized methodology (Bartosch, B., Dubuisson, J. and Cosset, F.-L. J. Exp. Med. 2003, 197:633-642) were made via a liposome-based transfection procedure of 293 T cells with plasmids expressing the murine leukemia virus capsid and polymerase proteins, an MLV genome encoding the luciferase reporter gene, and envelope glycoproteins from either HCV or vesicular stomatitis virus (VSV). The genotype 1a HCV E1 and E2 envelope coding sequences were derived from the H77C isolate (GenBank accession number AF009606). Media containing pseudoparticles was collected 3 days following transfection, filtered, and stored at −20° C. as a viral stock. Infections were performed in 384-well plates by mixing pseudovirus with 1×10⁴ Huh7 cells/well in the presence or absence of test inhibitors, followed by incubation at 37° C. Luciferase activity, reflecting the degree of entry of the pseudoparticles into host cells, was measured 2 days after infection. The specificity of the compounds for inhibiting HCV was determined by evaluating inhibition of VSV pseudoparticle infection.

Compounds and Data Analysis.

Test compounds were serially diluted 3-fold in dimethyl sulfoxide (DMSO) to give a final concentration range in the assay of 50.0 μM to 0.04 μM. Maximum activity (100% of control) and background were derived from control wells containing DMSO but no inhibitor or from uninfected wells, respectively. The individual signals in each of the compound test wells were then divided by the averaged control values after background subtraction and multiplied by 100% to determine percent activity. Assays were performed in duplicate and average EC₅₀ values (reflecting the concentration at which 50% inhibition of virus replication was achieved) were calculated. Compound EC₅₀ data is expressed as A:=≦100 nM; B=100-1000 nM. Representative data for compounds are reported in Table 1.

TABLE 1 EC₅₀ EC₅₀ Number Structure (nM) (nM) 1001

907 B 1002

215 B 1003

0.21 A 1004

0.49 A 1005

0.38 A 1006

0.45 A 1007

0.19 A 2001

1.34 A 2002

0.81 A 2003

0.76 A 2004

396 B 2005

184 B 2006

326 B

Pharmaceutical Compositions and Methods of Treatment

The compounds demonstrate activity against HCV NS5B and can be useful in treating HCV and HCV infection. Therefore, another aspect of the invention is a composition comprising a compound, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.

Another aspect of the invention is a composition further comprising a compound having anti-HCV activity.

Another aspect of the invention is a composition where the compound having anti-HCV activity is an interferon. Another aspect of the invention is where the interferon is selected from interferon alpha 2B, pegylated interferon alpha, consensus interferon, interferon alpha 2A, and lymphoblastoid interferon tau.

Another aspect of the invention is a composition where the compound having anti-HCV activity is a cyclosporin. Another aspect of the invention is where the cyclosporin is cyclosporin A.

Another aspect of the invention is a composition where the compound having anti-HCV activity is selected from the group consisting of interleukin 2, interleukin 6, interleukin 12, a compound that enhances the development of a type 1 helper T cell response, interfering RNA, anti-sense RNA, Imiqimod, ribavirin, an inosine 5′-monophospate dehydrogenase inhibitor, amantadine, and rimantadine.

Another aspect of the invention is a composition where the compound having anti-HCV activity is effective to inhibit the function of a target selected from HCV metalloprotease, HCV serine protease, HCV polymerase, HCV helicase, HCV NS4B protein, HCV entry, HCV assembly, HCV egress, HCV NS5A protein, IMPDH, and a nucleoside analog for the treatment of an HCV infection.

Another aspect of the invention is a composition comprising a compound, or a pharmaceutically acceptable salt thereof, a pharmaceutically acceptable carrier, an interferon and ribavirin.

Another aspect of the invention is a method of inhibiting the function of the HCV replicon comprising contacting the HCV replicon with a compound or a pharmaceutically acceptable salt thereof.

Another aspect of the invention is a method of inhibiting the function of the HCV NS5B protein comprising contacting the HCV NS5B protein with a compound or a pharmaceutically acceptable salt thereof.

Another aspect of the invention is a method of treating an HCV infection in a patient comprising administering to the patient a therapeutically effective amount of a compound or a pharmaceutically acceptable salt thereof. In another embodiment the compound is effective to inhibit the function of the HCV replicon. In another embodiment the compound is effective to inhibit the function of the HCV NS5B protein.

Another aspect of the invention is a method of treating an HCV infection in a patient comprising administering to the patient a therapeutically effective amount of a compound, or a pharmaceutically acceptable salt thereof, in conjunction with (prior to, after, or concurrently) another compound having anti-HCV activity.

Another aspect of the invention is the method where the other compound having anti-HCV activity is an interferon.

Another aspect of the invention is the method where the interferon is selected from interferon alpha 2B, pegylated interferon alpha, consensus interferon, interferon alpha 2A, and lymphoblastoid interferon tau.

Another aspect of the invention is the method where the other compound having anti-HCV activity is a cyclosporin.

Another aspect of the invention is the method where the cyclosporin is cyclosporin A.

Another aspect of the invention is the method where the other compound having anti-HCV activity is selected from interleukin 2, interleukin 6, interleukin 12, a compound that enhances the development of a type 1 helper T cell response, interfering RNA, anti-sense RNA, Imiqimod, ribavirin, an inosine 5′-monophospate dehydrogenase inhibitor, amantadine, and rimantadine.

Another aspect of the invention is the method where the other compound having anti-HCV activity is effective to inhibit the function of a target selected from the group consisting of HCV metalloprotease, HCV serine protease, HCV polymerase, HCV helicase, HCV NS4B protein, HCV entry, HCV assembly, HCV egress, HCV NS5A protein, IMPDH, and a nucleoside analog for the treatment of an HCV infection.

Another aspect of the invention is the method where the other compound having anti-HCV activity is effective to inhibit the function of target in the HCV life cycle other than the HCV NS5B protein.

“Therapeutically effective” means the amount of agent required to provide a meaningful patient benefit as understood by practitioners in the field of hepatitis and HCV infection.

“Patient” means a person infected with the HCV virus and suitable for therapy as understood by practitioners in the field of hepatitis and HCV infection.

“Treatment,” “therapy,” “regimen,” “HCV infection,” and related terms are used as understood by practitioners in the field of hepatitis and HCV infection.

The compounds of this invention are generally given as pharmaceutical compositions comprised of a therapeutically effective amount of a compound or its pharmaceutically acceptable salt and a pharmaceutically acceptable carrier and may contain conventional excipients. Pharmaceutically acceptable carriers are those conventionally known carriers having acceptable safety profiles. Compositions encompass all common solid and liquid forms including for example capsules, tablets, losenges, and powders as well as liquid suspensions, syrups, elixers, and solutions. Compositions are made using common formulation techniques, and conventional excipients (such as binding and wetting agents) and vehicles (such as water and alcohols) are generally used for compositions. See, for example, Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pa., 17th edition, 1985.

Solid compositions are normally formulated in dosage units and compositions providing from about 1 to 1000 mg of the active ingredient per dose are preferred. Some examples of dosages are 1 mg, 10 mg, 100 mg, 250 mg, 500 mg, and 1000 mg. Generally, other agents will be present in a unit range similar to agents of that class used clinically. Typically, this is 0.25-1000 mg/unit.

Liquid compositions are usually in dosage unit ranges. Generally, the liquid composition will be in a unit dosage range of 1-100 mg/mL. Some examples of dosages are 1 mg/mL, 10 mg/mL, 25 mg/mL, 50 mg/mL, and 100 mg/mL. Generally, other agents will be present in a unit range similar to agents of that class used clinically. Typically, this is 1-100 mg/mL.

The invention encompasses all conventional modes of administration; oral and parenteral methods are preferred. Generally, the dosing regimen will be similar to other agents used clinically. Typically, the daily dose will be 1-100 mg/kg body weight daily. Generally, more compound is required orally and less parenterally. The specific dosing regime, however, will be determined by a physician using sound medical judgement.

The invention also encompasses methods where the compound is given in combination therapy. That is, the compound can be used in conjunction with, but separately from, other agents useful in treating hepatitis and HCV infection. In these combination methods, the compound will generally be given in a daily dose of 1-100 mg/kg body weight daily in conjunction with other agents. The other agents generally will be given in the amounts used therapeutically. The specific dosing regime, however, will be determined by a physician using sound medical judgement.

Some examples of compounds suitable for compositions and methods are listed in Table 2.

TABLE 2 Type of Inhibitor or Brand Name Physiological Class Target Source Company NIM811 Cyclophilin Inhibitor Novartis Zadaxin Immuno-modulator Sciclone Suvus Methylene blue Bioenvision Actilon TLR9 agonist Coley (CPG10101) Batabulin (T67) Anticancer β-tubulin inhibitor Tularik Inc., South San Francisco, CA ISIS 14803 Antiviral antisense ISIS Pharmaceuticals Inc, Carlsbad, CA/Elan Phamaceuticals Inc., New York, NY Summetrel Antiviral antiviral Endo Pharmaceuticals Holdings Inc., Chadds Ford, PA GS-9132 (ACH- Antiviral HCV Inhibitor Achillion/Gilead 806) Pyrazolopyrimidine Antiviral HCV Inhibitors Arrow Therapeutics compounds and Ltd. salts From WO- 2005047288 26 May 2005 Levovirin Antiviral IMPDH inhibitor Ribapharm Inc., Costa Mesa, CA Merimepodib Antiviral IMPDH inhibitor Vertex (VX-497) Pharmaceuticals Inc., Cambridge, MA XTL-6865 (XTL- Antiviral monoclonal antibody XTL 002) Biopharmaceuticals Ltd., Rehovot, Isreal Telaprevir Antiviral NS3 serine protease Vertex (VX-950, LY- inhibitor Pharmaceuticals 570310) Inc., Cambridge, MA/Eli Lilly and Co. Inc., Indianapolis, IN HCV-796 Antiviral NS5B Replicase Wyeth/Viropharma Inhibitor NM-283 Antiviral NS5B Replicase Idenix/Novartis Inhibitor GL-59728 Antiviral NS5B Replicase Gene Labs/ Inhibitor Novartis GL-60667 Antiviral NS5B Replicase Gene Labs/ Inhibitor Novartis 2′C MeA Antiviral NS5B Replicase Gilead Inhibitor PSI 6130 Antiviral NS5B Replicase Roche Inhibitor R1626 Antiviral NS5B Replicase Roche Inhibitor 2′C Methyl Antiviral NS5B Replicase Merck adenosine Inhibitor JTK-003 Antiviral RdRp inhibitor Japan Tobacco Inc., Tokyo, Japan Levovirin Antiviral ribavirin ICN Pharmaceuticals, Costa Mesa, CA Ribavirin Antiviral ribavirin Schering-Plough Corporation, Kenilworth, NJ Viramidine Antiviral Ribavirin Prodrug Ribapharm Inc., Costa Mesa, CA Heptazyme Antiviral ribozyme Ribozyme Pharmaceuticals Inc., Boulder, CO BILN-2061 Antiviral serine protease Boehringer inhibitor Ingelheim Pharma KG, Ingelheim, Germany SCH 503034 Antiviral serine protease Schering Plough inhibitor Zadazim Immune modulator Immune modulator SciClone Pharmaceuticals Inc., San Mateo, CA Ceplene Immunomodulator immune modulator Maxim Pharmaceuticals Inc., San Diego, CA CellCept Immunosuppressant HCV IgG immuno- F. Hoffmann-La suppressant Roche LTD, Basel, Switzerland Civacir Immunosuppressant HCV IgG immuno- Nabi suppressant Biopharmaceuticals Inc., Boca Raton, FL Albuferon-α Interferon albumin IFN-α2b Human Genome Sciences Inc., Rockville, MD Infergen A Interferon IFN InterMune alfacon-1 Pharmaceuticals Inc., Brisbane, CA Omega IFN Interferon IFN-ω Intarcia Therapeutics IFN-β and EMZ701 Interferon IFN-β and EMZ701 Transition Therapeutics Inc., Ontario, Canada Rebif Interferon IFN-β1a Serono, Geneva, Switzerland Roferon A Interferon IFN-α2a F. Hoffmann-La Roche LTD, Basel, Switzerland Intron A Interferon IFN-α2b Schering-Plough Corporation, Kenilworth, NJ Intron A and Interferon IFN-α2b/α1-thymosin RegeneRx Zadaxin Biopharma. Inc., Bethesda, MD/ SciClone Pharmaceuticals Inc, San Mateo, CA Rebetron Interferon IFN-α2b/ribavirin Schering-Plough Corporation, Kenilworth, NJ Actimmune Interferon INF-γ InterMune Inc., Brisbane, CA Interferon-β Interferon Interferon-β-1a Serono Multiferon Interferon Long lasting IFN Viragen/ Valentis Wellferon Interferon Lympho-blastoid IFN- GlaxoSmithKline αn1 plc, Uxbridge, UK Omniferon Interferon natural IFN-α Viragen Inc., Plantation, FL Pegasys Interferon PEGylated IFN-α2a F. Hoffmann-La Roche LTD, Basel, Switzerland Pegasys and Interferon PEGylated IFN-α2a/ Maxim Ceplene immune modulator Pharmaceuticals Inc., San Diego, CA Pegasys and Interferon PEGylated IFN- F. Hoffmann-La Ribavirin α2a/ribavirin Roche LTD, Basel, Switzerland PEG-Intron Interferon PEGylated IFN-α2b Schering-Plough Corporation, Kenilworth, NJ PEG-Intron/ Interferon PEGylated IFN- Schering-Plough Ribavirin α2b/ribavirin Corporation, Kenilworth, NJ IP-501 Liver protection antifibrotic Indevus Pharmaceuticals Inc., Lexington, MA IDN-6556 Liver protection caspase inhibitor Idun Pharmaceuticals Inc., San Diego, CA ITMN-191 (R-7227) Antiviral serine protease InterMune inhibitor Pharmaceuticals Inc., Brisbane, CA GL-59728 Antiviral NS5B Replicase Genelabs Inhibitor ANA-971 Antiviral TLR-7 agonist Anadys Boceprevir Antiviral serine protease Schering Plough inhibitor TMS-435 Antiviral serine protease Tibotec BVBA, inhibitor Mechelen, Belgium BI-201335 Antiviral serine protease Boehringer inhibitor Ingelheim Pharma KG, Ingelheim, Germany MK-7009 Antiviral serine protease Merck inhibitor PF-00868554 Antiviral replicase inhibitor Pfizer ANA598 Antiviral Non-Nucleoside Anadys NS5B Polymerase Pharmaceuticals, Inhibitor Inc., San Diego, CA, USA IDX375 Antiviral Non-Nucleoside Idenix Replicase Inhibitor Pharmaceuticals, Cambridge, MA, USA BILB 1941 Antiviral NS5B Polymerase Boehringer Inhibitor Ingelheim Canada Ltd R&D, Laval, QC, Canada PSI-7851 Antiviral Nucleoside Pharmasset, Polymerase Inhibitor Princeton, NJ, USA PSI-7977 Antiviral Nucleotide NS5B Pharmasset, Polymerase Inhibitor Princeton, NJ, USA VCH-759 Antiviral NS5B Polymerase ViroChem Pharma Inhibitor VCH-916 Antiviral NS5B Polymerase ViroChem Pharma Inhibitor GS-9190 Antiviral NS5B Polymerase Gilead Inhibitor Peg-interferon Antiviral Interferon ZymoGenetics/Bristol- lamda Myers Squibb

Synthetic Methods

The compounds may be made by methods known in the art including those described below and including variations within the skill of the art. Some reagents and intermediates are known in the art. Other reagents and intermediates can be made by methods known in the art using readily available materials. The variables (e.g. numbered “R” substituents) used to describe the synthesis of the compounds are intended only to illustrate how to make the compounds and are not to be confused with variables used in the claims or in other sections of the specification. The following methods are for illustrative purposes and are not intended to limit the scope of the invention.

Abbreviations used in the schemes generally follow conventions used in the art. Chemical abbreviations used in the specification and examples are defined as follows: “NaHMDS” for sodium bis(trimethylsilyl)amide; “DMF” for N,N-dimethylformamide; “MeOH” for methanol; “NBS” for N-bromosuccinimide; “Ar” for aryl; “TFA” for trifluoroacetic acid; “LAH” for lithium aluminum hydride; “BOC”, “DMSO” for dimethylsulfoxide; “h” for hours; “rt” for room temperature or retention time (context will dictate); “min” for minutes; “EtOAc” for ethyl acetate; “THF” for tetrahydrofuran; “EDTA” for ethylenediaminetetraacetic acid; “Et₂O” for diethyl ether; “DMAP” for 4-dimethylaminopyridine; “DCE” for 1,2-dichloroethane; “ACN” for acetonitrile; “DME” for 1,2-dimethoxyethane; “HOBt” for 1-hydroxybenzotriazole hydrate; “DIEA” for diisopropylethylamine, “Nf” for CF₃(CF₂)₃SO₂—; and “TMOF” for trimethylorthoformate.

Abbreviations are defined as follows: “1×” for once, “2×” for twice, “3×” for thrice, “° C.” for degrees Celsius, “eq” for equivalent or equivalents, “g” for gram or grams, “mg” for milligram or milligrams, “L” for liter or liters, “mL” for milliliter or milliliters, “μL” for microliter or microliters, “N” for normal, “M” for molar, “mmol” for millimole or millimoles, “min” for minute or minutes, “h” for hour or hours, “rt” for room temperature, “RT” for retention time, “atm” for atmosphere, “psi” for pounds per square inch, “conc.” for concentrate, “sat” or “sat'd” for saturated, “MW” for molecular weight, “mp” for melting point, “ee” for enantiomeric excess, “MS” or “Mass Spec” for mass spectrometry, “ESI” for electrospray ionization mass spectroscopy, “HR” for high resolution, “HRMS” for high resolution mass spectrometry, “LCMS” for liquid chromatography mass spectrometry, “HPLC” for high pressure liquid chromatography, “RP HPLC” for reverse phase HPLC, “TLC” or “tlc” for thin layer chromatography, “NMR” for nuclear magnetic resonance spectroscopy, “¹H” for proton, “δ” for delta, “s” for singlet, “d” for doublet, “t” for triplet, “q” for quartet, “m” for multiplet, “br” for broad, “Hz” for hertz, and “α”, “β”, “R”, “S”, “E”, and “Z” are stereochemical designations familiar to one skilled in the art.

Synthetic Methods

LC/MS Method (i.e., Compound Identification).

All Liquid Chromatography (LC) data were recorded on a Shimadzu LC-10AS or LC-20AS liquid chromotograph using a SPD-10AV or SPD-20A UV-Vis detector and Mass Spectrometry (MS) data were determined with a Micromass Platform for LC in electrospray mode.

HPLC Method (i.e., Compound Isolation).

Compounds purified by preparative HPLC were diluted in methanol (1.2 mL) and purified using a Shimadzu LC-8A or LC-10A automated preparative HPLC system.

Preparation of Compound 1001

Step 1: NaHMDS (41 mL, 1M in THF) was added into the solution of 4,6-dichloro-2-(methylthio)pyrimidine (4 g) and tert-butyl 4-aminobenzoate (3.96 g) in THF (200 mL). The reaction was stirred at room temperature for 16 hours, before being quenched by water (100 mL). The aqueous layer was extracted with EtOAc (3×100 mL)). The combined organic phase was dried over MgSO₄ and concentrated under vacuum to give tert-butyl 4-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)benzoate which will be used without purification.

tert-butyl 4-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)benzoate MS (M + H)⁺ Calcd. 352.1 MS (M + H)⁺ Observ. 352.2 Retention Time 2.10 minutes LC Condition Solvent A 5% ACN:95% Water:10 mM Ammonium Actetate Solvent B 95% ACN:5% Water:10 mM Ammonium Actetate Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair ACN:Water:Ammonium Actetate Column Phenomenex LUNA C18, 30 × 2, 3 u

Step 2: A mixture of t-butyl 4-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)benzoate (300 mg) and 3,3′-(butane-1,4-diylbis(oxy))dipropan-1-amine (8.71 g) was heated to 115° C. for 16 hours. The reaction was quenched with water (100 mL). The aqueous layer was extracted with EtOAc (3×100 mL). The combined organic layer was dried over MgSO₄ and concentrated to offer tert-butyl 4-(6-(3-(4-(3-aminopropoxy)butoxy)propylamino)-2-(methylthio)pyrimidin-4-ylamino)benzoate which will used in the next step without purification.

tert-butyl 4-(6-(3-(4-(3-aminopropoxy)butoxy)propylamino)-2- (methylthio)pyrimidin-4-ylamino)benzoate MS (M + H)⁺ Calcd. 520.3 MS (M + H)⁺ Observ. 520.4 Retention Time 1.74 minutes LC Condition Solvent A 5% ACN:95% Water:10 mM Ammonium Actetate Solvent B 95% ACN:5% Water:10 mM Ammonium Actetate Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair ACN:Water:Ammonium Actetate Column Phenomenex LUNA C18, 30 × 2, 3 u

Step 3: TFA (3 mL) was added into the solution of tert-butyl 4-(6-(3-(4-(3-aminopropoxy)butoxy)propylamino)-2-(methylthio)pyrimidin-4-ylamino)benzoate (100 mg) in CH₂Cl₂ (10 mL). The reaction was stirred at room temperature for 3 days. Removal of solvents under vacuum offered 4-(6-(3-(4-(3-aminopropoxy)butoxy)propylamino)-2-(methylthio)pyrimidin-4-ylamino)benzoic acid which will be used in the next step without purification.

4-(6-(3-(4-(3-aminopropoxy)butoxy)propylamino)-2- (methylthio)pyrimidin-4-ylamino)benzoic acid MS (M + H)⁺ Calcd. 464.2 MS (M + H)⁺ Observ. 464.4 Retention Time 1.25 minutes LC Condition Solvent A 5% ACN:95% Water:10 mM Ammonium Actetate Solvent B 95% ACN:5% Water:10 mM Ammonium Actetate Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair ACN:Water:Ammonium Actetate Column Phenomenex LUNA C18, 30 × 2, 3 u

Step 4: To a solution of 4-(6-(3-(4-(3-aminopropoxy)butoxy)propylamino)-2-(methylthio)pyrimidin-4-ylamino)benzoic acid (250 mg) and TBTU (173 mg) was added iPr₂NEt (279 mg). The mixture was stirred at room temperature for 4 hours. DMF was removed under vacuum and the residue was purified by preparative HPLC to give 1001-In-01.

1001-In-01 MS (M + H)⁺ Calcd. 446.2 MS (M + H)⁺ Observ. 446.1 Retention Time 3.11 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 0 Final % B 100 Gradient Time 4 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 50 mm 3 um NMR 1H NMR (500 MHz, δ ppm 7.85 (d, 2H, J = 8.5 Hz), 7.52 (s, 1H), CDCl₃) 7.34 (d, 2H, J = 8.5 Hz), 5.81 (s, 1H), 3.73-3.30 (m, 12H), 2.56 (s, 3H), 1.93-1.67 (m, 8H)

Step 5: To a solution of 1001-In-01 (40 mg) in DCM (5 mL) was added mCPBA (40 mg, 77%). The mixture was stirred at room temperature for 16 hours. The mixture was diluted with the EtOAc (100 mL) and washed with water (30 mL), brine (30 mL), dried over MgSO₄ and concentrated under vacuum. The residue, 1001-In-02 was used for next step reaction without further purification.

1001-In-02 MS (M + H)⁺ Calcd. 478.2 MS (M + H)⁺ Observ. 478.4 Retention Time 2.27 minutes LC Condition Solvent A 5% ACN:95% Water:10 mM Ammonium Actetate Solvent B 95% ACN:5% Water:10 mM Ammonium Actetate Start % B 0 Final % B 100 Gradient Time 4 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:Ammonium Actetate Column Phenomenex LUNA C18, 50 × 2, 3 u

Step 6: To a solution of 2,2,2-trifluoroethanol (6.28 mg) and NaH (2.51 mg) in THF (2 mL) was added 1001-In-02 (6 mg). The mixture was stirred at room temperature for 16 hours. The reaction was quenched with water and extracted with EtOAc (2×30 mL). The organic layers were combined and concentrated. The residue was purified by preparative HPLC to give 1001 (2.4 mg).

1001 MS (M + H)⁺ Calcd. 498.2 MS (M + H)⁺ Observ. 498.1 Retention Time 2.69 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 30 Final % B 100 Gradient Time 4 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 50 mm 3 um NMR 1H NMR (500 MHz, δ ppm 7.85 (d, 2H, J = 8.5 Hz), 7.44 (d, 2H, CD₃OD) J = 8.5 Hz), 5.84 (s, 1H), 5.00 (m, 2H), 3.75-3.20 (m, 12H), 1.95-1.37 (m, 8H)

Preparation of Compound 1002

Step 1: A mixture of 4,6-dichloro-2-(methylthio)pyrimidine (1 g), ethyl 6-aminonicotinate (0.85 g) and NaHMDS (10.3 mL, 1M in THF) in THF (50 mL) was stirred at room temperature for 16 hours. The mixture was diluted with water and extracted with EtOAc (2×150 mL). The organic layers were combined, washed with brine (50 mL), dried over MgSO₄ and concentrated to give ethyl 6-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)nicotinate which was used as was.

ethyl 6-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)nicotinate MS (M + H)⁺ Calcd. 325.0 MS (M + H)⁺ Observ. 325.0 Retention Time 3.70 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 50 Final % B 100 Gradient Time 4 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 50 mm 3 um

Step 2: A crude of ethyl 6-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)nicotinate (400 mg) and K₂CO₃ (340 mg) in acetone (4 mL)/water (2 mL) was heated at 100° C. for 16 hours. After cooling to room temperature, the precipitate 6-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)nicotinic acid (280 mg) was collected and was used as was.

6-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)nicotinic acid MS (M + H)⁺ Calcd. 297.0 MS (M + H)⁺ Observ. 297.1 Retention Time 1.74 minutes LC Condition Solvent A 5% ACN:95% Water:10 mm Ammonium Actetate Solvent B 95% ACN:5% Water:10 mm Ammonium Actetate Start % B 0 Final % B 100 Gradient Time 4 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:Ammonium Actetate Column Phenomenex LUNA C18, 50 × 2, 3 u

Step 3: A mixture of 6-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)nicotinic acid (280 mg) and 3,3′-(butane-1,4-diylbis(oxy))dipropan-1-amine (1928 mg) was heated at 100° C. for 16 hours. After cooling to room etmperature, the mixture was diluted with EtOAc (200 mL), washed with H₂O (100 mL), brine (100 mL), and dried over MgSO₄ and concentrated. The residue was purified by preparative HPLC to give 6-(6-(3-(4-(3-aminopropoxy)butoxy)propylamino)-2-(methylthio)pyrimidin-4-ylamino)nicotinic acid (40 mg).

6-(6-(3-(4-(3-aminopropoxy)butoxy)propylamino)-2- (methylthio)pyrimidin-4-ylamino)nicotinic acid MS (M + H)⁺ Calcd. 465.2 MS (M + H)⁺ Observ. 465.1 Retention Time 1.84 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 30 Final % B 100 Gradient Time 4 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 50 mm 3 um

Step 4: To a solution of 6-(6-(3-(4-(3-aminopropoxy)butoxy)propylamino)-2-(methylthio)pyrimidin-4-ylamino)nicotinic acid (35 mg) and TBTU (24.2 mg) was added iPr₂NEt (38.9 mg). The mixture was stirred at room temperature for 4 hours. DMF was removed under vacuum and the residue was purified by preparative HPLC to give 1002-In-01 (20 mg).

1002-In-01 MS (M + H)⁺ Calcd. 447.2 MS (M + H)⁺ Observ. 447.1 Retention Time 2.46 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 30 Final % B 100 Gradient Time 4 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 50 mm 3 um NMR 1H NMR (500 MHz, δ ppm 8.63 (1H, s), 8.21 (d, 1H, J = 8.5 Hz), CD₃OD) 7.83 (s, 1H), 7.60 (s, 1H), 7.20 (d, 1H, J = 9.0 Hz), 3.74-3.33 (m, 12H), 2.64 (s, 3H), 1.96-1.66 (m, 8H)

Step 5: To a solution of 1002-In-01 (15 mg) in DCM (1 mL) was added mCPBA (11.3 mg). The mixture was stirred at room temperature for 3 hours. The mixture was diluted with the EtOAc (30 mL) and washed with water (10 mL), brine (10 mL), dried over MgSO₄ and concentrated under vacuum. The residue, 1002-In-02, was used for next step reaction without purification.

Step 6: To a solution of 2,2,2-trifluoroethanol (15.7 mg) and NaH (6.3 mg) in THF (2 mL) was added 0002-In-02 (15 mg). The mixture was stirre at room temperature for 16 hours. The reaction was quenched with water and slovents were removed under vacuum. The residue was purified by preparative HPLC to give 1002 (8 mg).

1002 MS (M + H)⁺ 499.2 Calcd. MS (M + H)⁺ 499.1 Observ. Retention Time 3.27 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 30 Final % B 100 Gradient Time 4 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 50 mm 3 um NMR 1H NMR (500 δ ppm 8.62 (1H, s), 8.16 (d, 1H, J = 8.5 Hz), 7.68 (s, MHz, CD₃OD) 1H), 7.65 (s, 1H), 7.09 (d, 1H, J = 9.0 Hz), 4.86 (m, 2H), 3.74-3.33 (m, 12H), 1.96-1.67 (m, 8H)

Preparation of Compound 1003

Step 1: NaHMDS (65.7 mL, 1M in THF) was added into the solution of 4,6-dichloro-2-(methylthio)pyrimidine (6.4 g) and methyl 4-aminobenzoate (5 g) in THF (200 mL). The reaction was stirred at room temperature for 16 hours, before being quenched by water. The aqueous layer was extracted with EtOAc (3×200 mL). The combined organic phase was dried over MgSO₄ and concentrated under vacuum to give the crude product, methyk 6-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)nicotinate, which was used in the next step without purification.

Methyl 6-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)nicotinate MS (M + H)⁺ Calcd. 311.0 MS (M + H)⁺ Observ. 311.1 Retention Time 1.83 minutes LC Condition Solvent A 5% ACN:95% Water:10 mM Ammonium Actetate Solvent B 95% ACN:5% Water:10 mM Ammonium Actetate Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair ACN:Water:Ammonium Actetate Column Phenomenex LUNA C18, 30 × 2, 3 u

Step 2: iPr₂NEt was added into a solution of methyl 6-((6-chloro-2-(methylthio)pyrimidin-4-yl)amino)nicotinate (500 mg) and 4-(aminomethyl)phenol (238 mg) in dioxane (20 mL). The reaction was stirred at 115° C. for 16 hours, before being quenched by water. The aqueous layer was extracted with EtOAc (3×20 mL). The combined organic phase was dried over MgSO₄ and concentrated under vacuum to give the crude product which was used without purification.

methyl 6-(6-(4-hydroxybenzylamino)-2-(methylthio)pyrimidin-4- ylamino)nicotinate MS (M + H)⁺ Calcd. 398.1 MS (M + H)⁺ Observ. 398.3 Retention Time 1.60 minutes LC Condition Solvent A 5% ACN:95% Water:10 mM Ammonium Actetate Solvent B 95% ACN:5% Water:10 mM Ammonium Actetate Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair ACN:Water:Ammonium Actetate Column Phenomenex LUNA C18, 30 × 2, 3 u

Step 3: mCPBA (1.02 g, 77%) was added into the solution of crude methyl 6-((6-((4-hydroxybenzyl)amino)-2-(methylthio)pyrimidin-4-yl)amino)nicotinate (0.9 g) in CH₂Cl₂ (10 mL). The reaction was stirred at room temperature for 2 hours to give 2-(6-(4-hydroxybenzylamino)-2-(methylsulfonyl)pyrimidin-4-ylamino)-5-(methoxycarbonyl)pyridine 1-oxide and methyl 6-(6-(4-hydroxybenzylamino)-2-(methylsulfonyl)pyrimidin-4-ylamino)nicotinate, before being quenched by water. The aqueous layer was extracted with EtOAc (3×20 mL). The combined organic phase was dried over MgSO₄ and concentrated under vacuum to give the crude product which was used as was.

2-(6-(4-hydroxybenzylamino)-2-(methylsulfonyl)pyrimidin-4-ylamino)-5- (methoxycarbonyl)pyridine 1-oxide MS (M + H)⁺ Calcd. 446.1 MS (M + H)⁺ Observ. 446.1 Retention Time 1.57 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

methyl 6-(6-(4-hydroxybenzylamino)-2-(methylsulfonyl)pyrimidin-4- ylamino)nicotinate MS (M + H)⁺ Calcd. 430.1 MS (M + H)⁺ Observ. 430.1 Retention Time 1.66 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Step 4: 2,2,2-trifluoroethanol (116 mg) and NaH (47 mg, 60%) were added into the solution of the crude products (50 mg) of Step 3 in THF (10 mL). The reaction was stirred at room temperature for 72 hours before being quenched by water. The aqueous layer was extracted with EtOAc (3×20 mL). The combined organic phase was dried over MgSO₄ and concentrated under vacuum to give a mixture of products, 2-(6-(4-hydroxybenzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)-5-(methoxycarbonyl)pyridine 1-oxide and methyl 6-(6-(4-hydroxybenzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinate, which was used as was.

2-(6-(4-hydroxybenzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4- ylamino)-5-(methoxycarbonyl)pyridine 1-oxide MS (M + H)⁺ Calcd. 466.1 MS (M + H)⁺ Observ. 466.1 Retention Time 2.04 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

methyl 6-(6-(4-hydroxybenzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin- 4-ylamino)nicotinate MS (M + H)⁺ Calcd. 450.1 MS (M + H)⁺ Observ. 450.1 Retention Time 1.85 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Step 5: PCl₃ (764 mg) was added into the solution of the crude mixture (1 g) from Step 4 in EtOAc. The reaction was stirred for 30 minutes, before being quenched by NaHCO₃. After solvents were removed under vacuum, the residue containing methyl 6-(6-(4-(phosphonooxy)benzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinate and methyl 6-(6-(4-hydroxybenzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinate was used as was.

methyl 6-(6-(4-(phosphonooxy)benzylamino)-2-(2,2,2- trifluoroethoxy)pyrimidin-4-ylamino)nicotinate MS (M + H)⁺ Calcd. 514.1 MS (M + H)⁺ Observ. 514.1 Retention Time 1.82 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Step 6: K₂CO₃ (5 g) was added into the solution of the whole crude mixture of Step 6 in MeOH (10 mL) and water (10 mL). The reaction was run at room temperature for 72 hours. Methanol was removed under vacumm. The aqueous layer was extracted with EtOAc (3×100 mL). The combined organic phase was dried over MgSO₄ and concentrated under vacuum to give the crude 6-(6-(4-hydroxybenzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinic acid which will be used without purification.

6-(6-(4-hydroxybenzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4- ylamino)nicotinic acid MS (M + H)⁺ Calcd. 436.1 MS (M + H)⁺ Observ. 436.1 Retention Time 1.75 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Step 7: iPr₂NEt (0.5 mL) was added into a solution of 6-((6-((4-hydroxybenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinic acid (340 mg), tert-butyl (3-amino-2,2-dimethylpropyl)carbamate (316 mg) and TBTU (501 mg) in THF (10 mL). The reaction was stirred at room temperature for 16 hours before being quenched by water (10 mL). The aqueous layer was extracted with EtOAc (3×10 mL). The combined organic phase was dried over MgSO₄ and concentrated under vacuum to give the crude product, tert-butyl 3-(6-(6-(4-hydroxybenzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinamido)-2,2-dimethylpropylcarbamate, which was purified by silica gel chromatography.

tert-butyl 3-(6-(6-(4-hydroxybenzylamino)-2-(2,2,2-trifluoroethoxy)- pyrimidin-4-ylamino)nicotinamido)-2,2-dimethylpropylcarbamate MS (M + H)⁺ Calcd. 620.3 MS (M + H)⁺ Observ. 620.3 Retention Time 2.09 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 0 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Step 8: A suspenssion of tert-butyl (3-(6-((6-((4-hydroxybenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamido)-2,2-dimethylpropyl)carbamate (30 mg), 1,3-dibromopropane (14.7 mg) and K₂CO₃ (13.4 mg) in acetone (6 mL) was heated to reflux for 16 hours. The mixture was diluted with EtOAc (200 mL), washed with water (30 mL), brine (30 mL), dried over MgSO₄ and concentrated. The residue was purified by preparative HPLC to give desired product tert-butyl 3-(6-(6-(4-(3-bromopropoxy)benzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinamido)-2,2-dimethylpropylcarbamate (11 mg).

tert-butyl 3-(6-(6-(4-(3-bromopropoxy)benzylamino)-2-(2,2,2- trifluoroethoxy)pyrimidin-4-ylamino)nicotinamido)-2,2- dimethylpropylcarbamate MS (M + H)⁺ Calcd. 740.2 MS (M + H)⁺ Observ. 740.3 Retention Time 1.94 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 50 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Step 9: To a solution of tert-butyl (3-(6-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamido)-2,2-dimethylpropyl)carbamate (10 mg) in DCM (3 mL) was added TFA (0.3 ml). The mixture was stirred at room temperature for 3 hours. All the solvents were removed under vacuum to give N-(3-amino-2,2-dimethylpropyl)-6-(6-(4-(3-bromopropoxy)benzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinamide (8 mg).

N-(3-amino-2,2-dimethylpropyl)-6-(6-(4-(3-bromopropoxy)benzylamino)- 2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinamide MS (M + H)⁺ Calcd. 640.2 MS (M + H)⁺ Observ. 640.2 Retention Time 1.19 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 50 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Step 10: A mixture of N-(3-amino-2,2-dimethylpropyl)-6-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamide (8 mg) and NaHCO₃ (1.05 mg) in MeCN (5 mL) was heated at 85° C. in a sealed tube for 16 hours. The solvent was removed under vacuum. The residue was purified by preparative HPLC to give 1003 (4 mg).

1003 MS (M + H)⁺ Calcd. 560.3 MS (M + H)⁺ Observ. 560.3 Retention Time 1.36 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 30 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Preparation of Compound 1004 and 1005

Step 1: A suspenssion of tert-butyl (3-(6-((6-((4-hydroxybenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamido)-2,2-dimethylpropyl)carbamate (90 mg), 3-chloro-2-(chloromethyl)prop-1-ene (27.2 mg) and K₂CO₃ (40.1 mg) in acetone (6 mL) was heated to reflux for 16 hours. The mixture was diluted with EtOAc (200 mL), washed with water (30 mL), brine (30 mL), dried over MgSO₄ and concentrated. The residue was purified by preparative HPLC to give desired product tert-butyl 3-(6-(6-(4-(2-(chloromethyl)allyloxy)benzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinamido)-2,2-dimethylpropylcarbamate (45 mg).

tert-butyl 3-(6-(6-(4-(2-(chloromethyl)allyloxy)benzylamino)-2-(2,2,2- trifluoroethoxy)pyrimidin-4-ylamino)nicotinamido)-2,2- dimethylpropylcarbamate MS (M + H)⁺ Calcd. 708.3 MS (M + H)⁺ Observ. 708.4 Retention Time 1.94 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 50 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Step 2: To a solution of tert-butyl (3-(6-((6-((4-((2-(chloromethyl)allyl)oxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamido)-2,2-dimethylpropyl)carbamate (45 mg) in DCM (3 mL) was added TFA (0.3 ml). The mixture was stirred at room temperature for 3 hours. All the solvents were removed under vacuum to give N-(3-amino-2,2-dimethylpropyl)-6-(6-(4-(2-(chloromethyl)allyloxy)benzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinamide (30 mg).

N-(3-amino-2,2-dimethylpropyl)-6-(6-(4-(2-(chloromethyl)allyloxy)- benzylamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-ylamino)nicotinamide MS (M + H)⁺ Calcd. 608.2 MS (M + H)⁺ Observ. 608.3 Retention Time 1.18 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 50 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Step 3: A mixture of N-(3-amino-2,2-dimethylpropyl)-6-((6-((4-((2-(chloromethyl)allyl)oxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamide (30 mg) and NaHCO₃ (4.14 mg) in MeCN (5 mL) was heated at 85° C. in a sealed tube for 16 hours. The solvent was removed under vacuum. The residue was purified by preparative HPLC to give 1004 (17 mg).

1004 MS (M + H)⁺ Calcd. 572.3 MS (M + H)⁺ Observ. 572.3 Retention Time 1.44 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 30 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Step 4: Compound 1004 was hydrogenated under 1 atm of hydrogen and catalytic amount of Pd on carbon in MeOH over 16 hours. Solids were removed via filtration and the solvent was removed under vacuum. The residue was purified by preparative HPLC to give 1005 (6 mg).

1005 MS (M + H)⁺ Calcd. 574.3 MS (M + H)⁺ Observ. 574.3 Retention Time 1.47 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 30 Final % B 100 Gradient Time 2 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm 3 um

Example 2001

Step 1: To a solution of 2,4,6-trichloropyrimidine (5 g, 27.3 mmol) and Hunig's Base (9.52 mL, 54.5 mmol) in DMF (5 mL) was added 2,2,2-trifluoroethanol (2.73 g, 27.3 mmol). The mixture was heated at 80° C. for 1 h in microwave vial. The resulting mixture was quenched with water, extracted with ethyl acetate, dried over MgSO₄, concentrated to give a crude mixture (7 g) that was used in the next step without purification.

4,6-dichloro-2-(2,2,2-trifluoroethoxy)pyrimidine MS (M + H)⁺ Calcd. 247.0 MS (M + H)⁺ Observ. 247.0 Retention Time 2.50 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 0 Final % B 100 Gradient/Stop Time 3 min/4 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm S10 3 μM

Step 2: To a mixture of 4,6-dichloro-2-(2,2,2-trifluoroethoxy)pyrimidine (500 mg, 2.02 mmol) and tert-butyl 4-aminobenzoate (469 mg, 2.43 mmol) in THF (10 mL) solution was added Lithium bis(trimethylsilyl)amide 1M in THF (2.43 mL, 2.43 mmol) solution. The resulting mixture was stirred at 60° C. for 2 h. The reaction mixture was quenched with water, extracted with ethyl acetate, dried over MgSO₄, concentrated to give a crude that was purified by Biotage eluting with 12:1 then 4:1 hexane:ethyl acetate to give 150 mg of the desired product as a solid.

tert-butyl 4-((6-chloro-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzoate MS (M + H)⁺ Calcd. 404.70 MS (M + H)⁺ Observ. 404.10 Retention Time 3.19 min LC Condition Solvent A 90% Water-10% Methanol-0.1% TFA Solvent B 10% Water-90% Methanol-0.1% TFA Start % B 0 Final % B 100 Gradient/Stop Time 3 min/4 min Flow Rate 1 mL/min Wavelength 220 Solvent Pair Water-Methanol-TFA Column PHENOMENEX-LUNA 2.0 × 30 mm S10 3 μM

Step 3: To a solution of tert-butyl 4-((6-chloro-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzoate (210 mg, 0.52 mmol), and Hunig's Base (0.18 mL, 1.04 mmol) in THF (3 mL) was added 4-(aminomethyl)phenol (96 mg, 0.78 mmol). The resulting mixture was refluxed for 1 hour. After cooling to rt, the solvent was removed and the crude product was purified by silica gel chromatography using 20-40% EtOAc/Hexanes to give tert-butyl 4-((6-((4-hydroxybenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzoate (117 mg, 46%) as white solid.

tert-butyl 4-((6-((4-hydroxybenzyl)amino)-2- (2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzoate MS (M + H)⁺ Calcd. 491.5 MS (M + H)⁺ Observ. 491.1 Retention Time 1.20 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

Step 4: To a solution of tert-butyl 4-((6-((4-hydroxybenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzoate (100 mg, 0.20 mmol), 1,3-dibromoethane (123 mg, 0.61 mmol) in acetone (2 mL) was added potassium carbonate (56 mg, 0.41 mmol). The resulting solution was stirred for 16 h at reflux. After cooling to rt, the solvent was removed and the crude product was purified by Biotage eluting with 20-40% ethyl acetate in hexane to give tert-butyl 4-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzoate (90 mg, 72%) as white solid.

tert-butyl 4-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2- trifluoroethoxy)pyrimidin-4-yl)amino)benzoate MS (M + H)⁺ Calcd. 611.1 MS (M + H)⁺ Observ. 613.1 Retention Time 1.19 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

Step 5: Tert-butyl 4-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzoate (90 mg, 0.15 mmol) and 4 N HCl in dioxane (2 mL) were stirred for 10 mins then concentrated under vacuum to give 4-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzoic acid which was carried to the next step without purification.

4-((6-((4-(3-bromopropoxy)benzyl)amino)-2- (2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzoic acid MS (M + H)⁺ Calcd. 555.1 MS (M + H)⁺ Observ. 555.1 Retention Time 1.06 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

Step 6: To a solution of 4-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzoic acid (90 mg, 0.16 mmol), Hunig's Base (0.142 mL, 0.81 mmol) and tert-butyl (3-amino-2,2-dimethylpropyl)carbamate (39.3 mg, 0.19 mmol) in CH₂Cl₂ (2 mL) was added HATU (92 mg, 0.24 mmol). After stirring at room temperature for 1 h, the mixture was concentrated and purified by Biotage eluting with 20-50% ethyl acetate in hexane to give 100 mg of product (83%) as a white solid.

tert-butyl (3-(4-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2- trifluoroethoxy)pyrimidin-4-yl)amino)benzamido)-2,2- dimethylpropyl)carbamate MS (M + H)⁺ Calcd. 740.6 MS (M + H)⁺ Observ. 741.2 Retention Time 1.16 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

Step 7: tert-butyl (3-(4-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzamido)-2,2-dimethylpropyl)carbamate (100 mg, 0.14 mmol) was stirred in TFA/DCM (1:1) solution (2 mL) for 15 mins. The solution was concentrated under vacuum to give N-(3-amino-2,2-dimethylpropyl)-4-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzamide which was carried to the next step without purification.

N-(3-amino-2,2-dimethylpropyl)-4-((6-((4-(3- bromopropoxy)benzyl)amino)-2- (2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzamide MS (M + H)⁺ Calcd. 640.5 MS (M + H)⁺ Observ. 641.2 Retention Time 1.03 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

Step 8: To a solution of N-(3-amino-2,2-dimethylpropyl)-4-((6-((4-(3-bromopropoxy)benzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)benzamide (70 mg, 0.11 mmol) in ACN (2 mL) was added potassium carbonate (30 mg, 0.22 mmol). The mixture was heated in microwave reactor at 130° C. for 1 h. After cooling to rt, the mixture was filtered and white solid was washed with ACN. Pre-HPLC separation to give Compound 2001 (8 mg, 13%) as white solid.

¹H NMR (500 MHz, DMSO-d₆) δ 9.17 (s, 1H, NH), 8.83 (br. s., 1H, NH), 7.77 (t, J=5.5 Hz, 1H), 7.44 (d, J=8.5 Hz, 2H), 7.21 (d, J=8.5 Hz, 2H), 7.03 (d, J=8.9 Hz, 2H), 6.63 (d, J=8.5 Hz, 2H), 4.91 (d, J=9.2 Hz, 2H), 4.26 (d, J=5.5 Hz, 2H), 4.20 (t, J=6.4 Hz, 2H), 3.25 (d, J=5.2 Hz, 2H), 2.74 (d, J=4.3 Hz, 2H), 5.50 (m, 2H), 1.92 (s, 2H), 0.92 (s, 6H).

Example 2001 MS (M + H)⁺ Calcd. 559.6 MS (M + H)⁺ Observ. 559.2 Retention Time 1.04 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

Example 2002

The Example 2002 was prepared following the procedure reported in Example 2001. 4-(aminomethyl)-3-fluorophenol was used instead of 4-(aminomethyl)phenol in step 3.

Example 2002 MS (M + H)⁺ Calcd. 577.25 MS (M + H)⁺ Observ. 577.29 Retention Time 0.79 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

Example 2003

The Example 2003 was prepared following the procedure reported in Example 2001. 4-(aminomethyl)-2-fluorophenol was used instead of 4-(aminomethyl)phenol in step 3.

Example 2003 MS (M + H)⁺ Calcd. 577.25 MS (M + H)⁺ Observ. 577.26 Retention Time 0.77 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

Example 2004

The Example 2004 was prepared following the procedure reported in Example 2001. Tert-butyl((1-(aminomethyl)cyclopropyl)methyl)carbamate was used instead of tert-butyl (3-amino-2,2-dimethylpropyl)carbamate in step 6.

Example 2004 MS (M + H)⁺ Calcd. 557.58 MS (M + H)⁺ Observ. 557.24 Retention Time 0.87 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

Example 2005

The Example 2005 was prepared following the procedure reported in Example 2001. (R)-tert-butyl (3-amino-2-methylpropyl)carbamate was used instead of tert-butyl (3-amino-2,2-dimethylpropyl)carbamate in step 6.

Example 2005 MS (M + H)⁺ Calcd. 545.24 MS (M + H)⁺ Observ. 545.26 Retention Time 0.85 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

Example 2006

The Example 2006 was prepared following the procedure reported in Example 2001. Tert-butyl (4-amino-2-methylbutan-2-yl)carbamate was used instead of tert-butyl (3-amino-2,2-dimethylpropyl)carbamate in step 6.

Example 2006 MS (M + H)⁺ Calcd. 559.25 MS (M + H)⁺ Observ. 559.25 Retention Time 0.85 min LC Condition Solvent A 100% Water:0.05% TFA Solvent B 100% ACN:0.05% TFA Start % B 2 Final % B 98 Gradient Time 2.2 min Flow Rate 0.8 mL/min Wavelength 220 Solvent Pair ACN:Water:TFA Column Acquity UPLC BEH C18 1.7 μm

It will be evident to one skilled in the art that the present disclosure is not limited to the foregoing illustrative examples, and that it can be embodied in other specific forms without departing from the essential attributes thereof. It is therefore desired that the examples be considered in all respects as illustrative and not restrictive, reference being made to the appended claims, rather than to the foregoing examples, and all changes which come within the meaning and range of equivalency of the claims are therefore intended to be embraced therein. 

We claim:
 1. A compound of formula I

where Ar¹ is phenyl or pyridinyl substituted with 1 R²; R¹ is alkyl, hydroxyalkyl, alkoxyalkyl, haloalkyl, cycloalkyl, hydroxycycloalkyl, alkoxycycloalkyl, halocycloalkyl, cycloalkenyl, benzyl, indanyl, or alkylcarbonyl; R² is hydrogen, cyano, halo, alkyl, haloalkyl, alkoxy, or haloalkoxy; R³ is hydrogen, alkyl, (amino)alkyl, (alkylamino)alkyl, (dialkylamino)alkyl, ((alkylcarbonyl)amino)alkyl, ((haloalkylcarbonyl)amino)alkyl, ((alkoxycarbonyl)amino)alkyl, ((benzyloxycarbonyl)amino)alkyl, alkylcarbonyl, alkoxycarbonyl, benzyloxycarbonyl, aminocarbonyl, alkylaminocarbonyl, or dialkyaminocarbonyl; R⁴ is hydrogen, alkyl, (amino)alkyl, (alkylamino)alkyl, or (dialkylamino)alkyl; R⁵ is hydrogen, alkyl, (amino)alkyl, (alkylamino)alkyl, or (dialkylamino)alkyl; Q is an alkylene or alkenylene chain containing 0-6 groups selected from the group consisting of O, NR³, S, S(O), S(O₂), C(O)O, C(O)NR⁴, OC(O)NR⁴, NR⁴C(O)NR⁴, and Z, provided that any O or S atom does not directly bond to another O or S atom, such that ring A is 13-36 membered; and where the alkylene or alkenylene chain is substituted with 0-6 substituents selected from the group consisting of alkyl, alkylene, hydroxy, and alkoxy; X is O, CH₂, CO, CO₂, or C(O)NR⁵; and Z is C₃₋₇ cycloalkylene or phenylene; or a pharmaceutically acceptable salt thereof.
 2. A compound of claim 1 where Ar¹ is phenyl or pyridinyl substituted with 1 R²; R¹ is haloalkyl; R² is hydrogen or halo; R³ is hydrogen or alkyl; R⁵ is hydrogen or alkyl; Q is an alkylene or alkenylene chain containing 0-6 groups selected from the group consisting of O, NR³, and Z, provided that any O atom does not directly bond to another O atom, such that ring A is 13-36 membered; and where the alkylene or alkenylene chain is substituted with 0-6 substituents selected from the group consisting of alkyl and alkylene; X is C(O)NR⁵; and Z is C₃₋₇ cycloalkylene or phenylene; or a pharmaceutically acceptable salt thereof.
 3. A compound of claim 1 where Ar¹ is 1,4-benzenediyl or 1,4-dipyridindiyl substituted with 1 R²; R¹ is trifluoroethyl; R² is hydrogen or fluoro; R³ is hydrogen; R⁵ is hydrogen; Q is an alkylene or alkenylene chain containing 0-6 groups selected from the group consisting of O, NR³, and Z, provided that any O atom does not directly bond to another O atom, such that ring A is 13-36 membered; and where the alkylene or alkenylene chain is substituted with 0-6 substituents selected from the group consisting of methyl and methylene; X is C(O)NR⁵; and Z is C₃₋₇ cycloalkylene or phenylene; or a pharmaceutically acceptable salt thereof.
 4. A compound of claim 1 where Ar¹ is 1,4-benzenediyl substituted with 1 R²; or a pharmaceutically acceptable salt thereof.
 5. A compound of claim 1 where Ar¹ is 1,4-dipyridindiyl substituted with 1 R²; or a pharmaceutically acceptable salt thereof.
 6. A compound of claim 1 where Z is 1,4-phenylene; or a pharmaceutically acceptable salt thereof.
 7. A compound of claim 1 where Z is cyclopropylene; or a pharmaceutically acceptable salt thereof.
 8. A compound of claim 1 selected from the group consisting of

or a pharmaceutically acceptable salt thereof.
 9. A pharmaceutical composition comprising a compound of claim 1, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
 10. The pharmaceutical composition of claim 9 further comprising at least one additional compound having therapeutic benefits for HCV wherein the compound is selected from the group consisting of interferons, cyclosporins, interleukins, HCV metalloprotease inhibitors, HCV serine protease inhibitors, HCV polymerase inhibitors, HCV helicase inhibitors, HCV NS4B protein inhibitors, HCV entry inhibitors, HCV assembly inhibitors, HCV egress inhibitors, HCV NS5A protein inhibitors, HCV NS5B protein inhibitors, and HCV replicon inhibitors.
 11. A method of treating hepatitis C infection comprising administering a therapeutically effective amount of a compound of claim 1 to a patient.
 12. The method of claim 11 further comprising administering at least one additional compound having therapeutic benefits for HCV wherein the compound is selected from the group consisting of interferons, cyclosporins, interleukins, HCV metalloprotease inhibitors, HCV serine protease inhibitors, HCV polymerase inhibitors, HCV helicase inhibitors, HCV NS4B protein inhibitors, HCV entry inhibitors, HCV assembly inhibitors, HCV egress inhibitors, HCV NS5A protein inhibitors, HCV NS5B protein inhibitors, and HCV replicon inhibitors. 